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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • C12Q1/6869—Methods for sequencing
  • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
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  • B01L3/502—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures
  • B01L3/5027—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip
  • B01L3/502761—Containers for the purpose of retaining a material to be analysed, e.g. test tubes with fluid transport, e.g. in multi-compartment structures by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip specially adapted for handling suspended solids or molecules independently from the bulk fluid flow, e.g. for trapping or sorting beads, for physically stretching molecules
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  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
  • B01L—CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE
  • B01L2200/00—Solutions for specific problems relating to chemical or physical laboratory apparatus
  • B01L2200/06—Fluid handling related problems
  • B01L2200/0647—Handling flowable solids, e.g. microscopic beads, cells, particles
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  • B01L2300/08—Geometry, shape and general structure
  • B01L2300/0861—Configuration of multiple channels and/or chambers in a single devices
  • B01L2300/0877—Flow chambers
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  • B01—PHYSICAL OR CHEMICAL PROCESSES OR APPARATUS IN GENERAL
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  • C12Q2527/00—Reactions demanding special reaction conditions
  • C12Q2527/146—Concentration of target or template
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  • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
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  • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
  • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
  • C12Q2537/149—Sequential reactions

Definitions

• the present disclosure relates to, among other things, sequencing of polynucleotides.
• Sequencing of a template polynucleotide strand may occur through multiple cycles of reactions by which one detectable nucleotide per cycle is incorporated into a copy strand.
• the detectable nucleotides are typically blocked to prevent incorporation of more than one detectable nucleotide per cycle.
• a wash step is typically performed to remove any unincorporated detectable nucleotide.
• a detection step in which the identity of the detectable nucleotide incorporated into the copy strand is determined, may then be performed.
• an unblocking step and cleavage or masking step is performed in which the blocking agent is removed from the last incorporated nucleotide in the copy strand and the detectable moiety is cleaved from or masked on the last nucleotide incorporated into the copy strand.
• the detectable moiety serves as the blocking agent, and removal of the detectable moiety may remove the blocking agent.
• the cycle is then repeated by introducing detectable nucleotides in an incorporation step.
• clusters of template polynucleotide strands having the same sequence are simultaneously sequenced.
• the clusters serve to amplify the signal produced by detectable nucleotides incorporated into the copy strands. Because the clusters contain multiple template strands of the same sequence, the nucleotide incorporated into the corresponding copy strands at each round of nucleotide addition should be the same, and the signal from the detectable nucleotide should be enhanced proportional to the number of copies of the template strand in the cluster.
• a recent goal of sequencing of polynucleotides is to decrease the time to complete the sequencing while maintaining high fidelity.
• One way to achieve decreased sequencing time is to reduce the cycle time by shortening the duration of the incorporation step.
• a number of more efficient polymerases and modified nucleotides have been developed to provide more efficient incorporation of nucleotides into the copy strand.
• the incorporation step still tends to suffer from incomplete incorporation of nucleotides across all template strands being sequenced.
• the copy strand in which the nucleotide is not incorporated is said to be out of phase with those copy strands in which the nucleotide is incorporated during the incorporation step.
• the signal from a cluster may become too heterogeneous to determine the nucleotide that was incorporated into the in-phase copy strands.
• the present disclosure describes, among other things, polynucleotide sequencing methods that allow for short cycle times for incorporation of labeled nucleotides while reducing phasing.
• the methods include incubating unlabeled nucleotides with a cluster of template polynucleotide strands having the same sequence when the identity of the previously added labeled nucleotide is being detected.
• the detection step provides time for the addition of the unlabeled nucleotides to be incorporated into the copy strands in which the previously added labeled nucleotide did not get incorporated.
• all or most of the copy strands will be in phase and ready to incorporate the appropriate labeled nucleotide in the subsequent incorporate step.
• the polynucleotide sequencing method comprises introducing a chain extending enzyme and a mixture of blocked, labeled nucleotides to a flow cell comprising a site at which multiple template polynucleotide strands having the same nucleotide sequence are bound to a surface of the flow cell.
• the chain extending enzyme is configured to incorporate an appropriate one of the blocked, labeled nucleotides into copy polynucleotide strands, based on the sequence of the template strands to which the copy polynucleotide strands correspond.
• the method further comprises washing unincorporated blocked, labeled nucleotides away from the flow cell and introducing a composition comprising a mixture of blocked, unlabeled nucleotides to the flow cell during or after the washing away of the unincorporated blocked, labeled nucleotides from the flow cell.
• a blocked, unlabeled nucleotide of the mixture of the blocked, unlabeled nucleotides is available for incorporation into the copy polynucleotide strands, based on a sequence of the template strands to which the copy polynucleotide strands correspond, provided that the previously incorporated nucleotide in the copy strand, if any, is not blocked.
• the method also comprises detecting the identity of the one blocked, labeled nucleotide incorporated into the copy strands, if any, while the mixture of blocked, unlabeled nucleotides is incubated with the flow cell.
• the label and block may then be removed from the blocked, labeled nucleotide incorporated into the copy strands and the block may be removed from the blocked, unlabeled nucleotide, if any, incorporated into the copy strands.
• the process may then be repeated for a predetermined number of cycles or until the sequencing is complete.
• FIGS 1-2 are flow diagrams illustrating embodiments of sequences methods described herein.
• FIG 3 is a schematic plan view of an embodiment of a flow cell that may be employed in accordance with the teachings presented herein.
• FIGS. 4A-G are schematic drawings illustrating various cycles of sequencing and compensation for phasing during the scanning (detection) step.
• FIG 5 is a plot illustrating the correlation between phasing (phasing weight %) and PhiX error rate (ER/%) using an Illumina MiniSeqTM sequencer with different incorporation times (46 seconds, 23 seconds, and 12 seconds).
• FIG 6 is a plot of cumulative PhiX error rates over 80 cycles of sequencing in which no blocked, unlabeled nucleotides were used (standard scan mix) during a detection step or used blocked, unlabeled nucleotides were used (ScanAndFill mix) during the detection step.
• FIG 7 is a bar graph of phasing, prephasing, and %Q30 rates over 40 cycles of sequencing in which blocked, unlabeled nucleotides were used (ScanAndFill), with additional polymerase (Poll671) or no additional polymerase (No Pol), during the detection step.
• FIG 8 is a plot of signal decay (P90Red) observed over 100 cycles of sequencing in which blocked, unlabeled nucleotides (S&F) were used during the detection step in the presence and absence of 3 mM ascorbate, which protects DNA from oxidative damage caused by the optical scanning.
• FIG 9 is a plot of cumulative PhiX error rate (%Error, %Q30 - inset) observed over 100 cycles of sequencing in which blocked, unlabeled nucleotides (S&F) were used during the detection step in the presence and absence of 3 mM ascorbate.
• the term“or” is generally employed in its sense including“and/or” unless the content clearly dictates otherwise.
• the term“and/or” means one or all of the listed elements or a combination of any two or more of the listed elements.
• “providing” in the context of a compound, composition, or article means making the compound, composition, or article, purchasing the compound, composition or article, or otherwise obtaining the compound, composition or article.
• the term“chain extending enzyme” is an enzyme that produces a copy replicate of a polynucleotide using the polynucleotide as a template strand.
• the chain extending enzyme may be an enzyme having polymerase activity.
• DNA polymerases bind to the template strand and then move down the template strand sequentially adding nucleotides to the free hydroxyl group at the 3' end of a growing strand of nucleic acid.
• DNA polymerases typically synthesize complementary DNA molecules from DNA templates and RNA polymerases typically synthesize RNA molecules from DNA templates (transcription). Polymerases may use a short RNA or DNA strand, called a primer, to begin strand growth.
• Some polymerases may displace the strand upstream of the site where they are adding bases to a chain. Such polymerases are said to be strand displacing, meaning they have an activity that removes a complementary strand from a template strand being read by the polymerase.
• Exemplary polymerases having strand displacing activity include, without limitation, the large fragment of Bst (Bacillus stearothermophilus) polymerase, exo-Klenow polymerase or sequencing grade T7 exo-polymerase.
• Some polymerases have an activity that degrades the strand behind them (3' exonuclease activity). Some useful polymerases have been modified, either by mutation or otherwise, to reduce or eliminate 3' and/or 5' exonuclease activity.
• the term "primer” and its derivatives refer generally to any polynucleotide that may hybridize to a target sequence of interest.
• the primer functions as a substrate onto which nucleotides may be polymerized by a polymerase; in some embodiments, however, the primer may become incorporated into the synthesized polynucleotide strand and provide a site to which another primer may hybridize to prime synthesis of a new strand that is complementary to the synthesized nucleic acid molecule.
• the primer may be comprised of any combination of nucleotides or analogs thereof In some embodiments, the primer is a single- stranded oligonucleotide or polynucleotide.
• polynucleotide and“oligonucleotide” are used interchangeably herein to refer to a polymeric form of nucleotides of any length, and may comprise ribonucleotides, deoxyribonucleotides, analogs thereof, or mixtures thereof. This term refers only to the primary structure of the molecule. Thus, the term includes triple-, double- and single-stranded deoxyribonucleic acid (“DNA”), as well as triple-, double- and single-stranded ribonucleic acid (“RNA”).
• DNA triple-, double- and single-stranded deoxyribonucleic acid
• RNA triple-, double- and single-stranded ribonucleic acid
• amplified target sequences refers generally to a polynucleotide sequence produced by the amplifying the target sequences using target-specific primers and the methods provided herein.
• the amplified target sequences may be either of the same sense (i.e the positive strand) or antisense (i.e., the negative strand) with respect to the target sequences.
• Suitable nucleotides for use in the provided methods include, but are not limited to, deoxynucleotide triphosphates, deoxyadenosine triphosphate (dATP), deoxythymidine triphosphate (dTTP), deoxycytidine triphosphate (dCTP), and deoxyguanosine triphosphate (dGTP).
• the nucleotides used in the provided methods can include a blocking moiety such as a reversible terminator moiety that inhibits chain extension.
• Suitable labels for use on the labeled nucleotides include, but are not limited to, haptens, radionucleotides, enzymes, fluorescent labels, chemiluminescent labels, and chromogenic agents.
• a polynucleotide will generally contain phosphodiester bonds, although in some cases nucleic acid analogs can have alternate backbones, comprising, for example, phosphoramide (Beaucage et ah, Tetrahedron 49(10): 1925 (1993) and references therein; Letsinger, J. Org. Chem. 35:3800 (1970); Sblul et ah, Eur. J. Biochem. 81 :579 (1977); Letsinger et ah, Nucl. Acids Res. 14:3487 (1986); Sawai et al, Chem. Lett. 805 (1984), Letsinger et al., J. Am. Chem. Soc.
• a polynucleotide will generally contain a specific sequence of four nucleotide bases: adenine (A); cytosine (C); guanine (G); and thymine (T).
• Uracil (U) can also be present, for example, as a natural replacement for thymine when the nucleic acid is RNA. Uracil can also be used in DNA.
• a polynucleotide may also include native or non-native bases.
• a native deoxyribonucleic acid polynucleotide may have one or more bases selected from the group consisting of adenine, thymine, cytosine or guanine and a ribonucleic acid may have one or more bases selected from the group consisting of uracil, adenine, cytosine or guanine.
• a deoxyribonucleic acid polynucleotides used in the methods or compositions set forth herein may include, for example, uracil bases and a ribonucleic acid can include, for example, a thymine base.
• non-native bases that may be included in a nucleic acid, whether having a native backbone or analog structure, include, without limitation, inosine, xathanine, hypoxathanine, isocytosine, isoguanine, 2-aminopurine,
• isocytosine and isoguanine may be included in a nucleic acid in order to reduce non-specific hybridization, as generally described in U.S. Patent No. 5,681,702, which is incorporated by reference herein in its entirety.
• a non-native base used in a polynucleotide may have universal base pairing activity such that it is capable of base pairing with any other naturally occurring base.
• Exemplary bases having universal base pairing activity include 3-nitropyrrole and 5- nitroindole.
• Other bases that can be used include those that have base pairing activity with a subset of the naturally occurring bases such as inosine, which basepairs with cytosine, adenine or uracil.
• incorpora nucleotide into a polynucleotide strand refers to joining of the nucleotide to a free 3 ' hydroxyl group of the polynucleotide strand via formation of a phosphodiester linkage with the 5 ' phosphate group of the nucleotide.
• the polynucleotide template to be sequenced can be DNA or RNA, or even a hybrid molecule that includes both deoxynucleotides and ribonucleotides.
• the polynucleotide can include naturally occurring and/or non-naturally occurring nucleotides and natural or non-natural backbone linkages.
• the present disclosure describes, among other things, polynucleotide sequencing methods that allow for short cycle times for incorporation of labeled nucleotides while reducing phasing.
• the methods include incubating unlabeled nucleotides with a cluster of template polynucleotide strands having the same sequence when the identity of the previously added labeled nucleotide is being detected.
• the detection step provides time for the addition of the unlabeled nucleotides to be incorporated into the copy strands in which the previously labeled nucleotide from the previous incorporation step did not get incorporated.
• all or most of the copy strands will be in phase and ready to incorporate the appropriate labeled nucleotide in the subsequence incorporate step.
• the detection step tends to take substantially more time than the incorporation step, particularly if the detection step includes imaging. Accordingly, the detection step may provide substantially more time for nucleotide incorporation than the incorporation step, which may substantially reduce phasing due to lagging. Because the nucleotides incorporated into the lagging copy strands are unlabeled, they do not produce a signal during detection and thus do not interfere with detection.
• SBS techniques include, but are not limited to, the Genome Analyzer systems (Illumina Inc., San Diego, CA) and the True Single Molecule Sequencing (tSMS)TM systems (Helicos BioSciences Corporation, Cambridge, MA). Briefly, a number of sequencing by synthesis reactions are used to elucidate the identity of a plurality of bases at target positions within a target sequence. All of these reactions rely on the use of a target nucleic acid sequence having at least two domains; a first domain to which a sequencing primer will hybridize, and an adjacent second domain, for which sequence information is desired.
• extension enzymes Upon formation of an assay complex, extension enzymes are used to add deoxynucleotide triphosphates (dNTPs) to a sequencing primer that is hybridized to first domain, and each addition of dNTPs is read to determine the identity of the added dNTP. This may proceed for many cycles.
• SBS techniques such as, the Genome Analyzer systems (Illumina Inc., San Diego, CA) and the True Single Molecule Sequencing (tSMS)TM systems (Helicos BioSciences Corporation, Cambridge, MA), utilize labeled nucleotides to determine the sequence of a target nucleic acid molecule.
• a target nucleic acid molecule can be hybridized with a primer and incubated in the presence of a polymerase and a labeled nucleotide containing a blocking group.
• the primer is extended such that the nucleotide is incorporated.
• the presence of the blocking group permits only one round of incorporation, that is, the incorporation of a single nucleotide.
• the presence of the label permits identification of the incorporated nucleotide.
• a plurality of homogenous single nucleotide bases can be added during each cycle, such as used in the True Single Molecule Sequencing (tSMS)TM systems (Helicos BioSciences Corporation, Cambridge, MA) or, alternatively, all four nucleotide bases can be added during each cycle simultaneously, such as used in the Genome Analyzer systems (Illumina Inc., San Diego, CA), particularly when each base is associated with a distinguishable label. After identifying the incorporated nucleotide by its corresponding label, both the label and the blocking group can be removed, thereby allowing a subsequent round of incorporation and identification.
• tSMS True Single Molecule Sequencing
• Determining the identity of the added nucleotide base includes, in some embodiments, repeated exposure of the newly added labeled bases a light source that can induce a detectable emission due the addition of a specific nucleotide base, i.e. dATP, dCTP, dGTP or dTTP.
• a specific nucleotide base i.e. dATP, dCTP, dGTP or dTTP.
• the methods and compositions disclosed herein are particularly useful for such SBS techniques.
• the methods and compositions described herein may be particularly useful for sequencing from an array of nucleic acids, where multiple sequences can be read simultaneously from multiple positions on the array since each nucleotide at each position can be identified based on its identifiable label. Exemplary methods are described in US 2009/0088327; US 2010/0028885; and US 2009/0325172, each of which is incorporated herein by reference.
• the methods include introducing a first chain extending enzyme and a mixture of blocked, labeled nucleotides to a site comprising multiple template polynucleotide strands having the same nucleotide sequence (100).
• the first chain extending enzyme is configured to incorporate an appropriate one of the blocked, labeled nucleotides into copy polynucleotide strands, based on the sequence of the template strands to which the copy polynucleotide strands correspond.
• a polynucleotide primer may be hybridized to the template strand to facilitate sequencing from a predetermined starting position.
• the blocked, labeled nucleotides are incubated with the template strands and chain extending enzyme for a period of time in an“incorporation step.”
• the incorporation step may take any suitable amount of time. As the time of the incorporation step increases, phasing tends to decrease because sufficient time is provided for incorporation of a blocked, labeled nucleotide into a copy strand. However, longer incorporation steps prevent the common goal of faster sequencing.
• One advantage of the methods described herein is that the time of the incorporation step may be reduced to a level that results in a previously unacceptable level of phasing because lagging copy strands may be brought back into phase during a detection step. By reducing the time of the incorporation step, the time of the overall sequencing process may be reduced.
• the time that a composition comprising a mixture of blocked, labeled nucleotides is incubated with the template polynucleotides is between 1 second and 60 seconds, such as from 5 seconds to 45 sections, or from 10 seconds to 30 seconds. In some embodiments, the time that a composition comprising a mixture of blocked, labeled nucleotides with the template polynucleotides is 15 seconds or less, such as 10 seconds or less, or 7.5 seconds or less.
• the incorporation step is sufficiently long to allow for incorporation of blocked, labeled nucleotide in a sufficient number of copy strands to produce a detectable signal during a detection step.
• the unincorporated blocked, labeled nucleotides may be washed away from the site (110), and a composition comprising a mixture of blocked, unlabeled nucleotides may be introduced to the site comprising the multiple template polynucleotide strands (120).
• the introduction of the composition comprising the mixture of blocked, unlabeled nucleotides (step 120) serves to wash away the unincorporated blocked, labeled nucleotides (step 110).
• the presence of a separate wash step (110) may, in some embodiments, be preferable.
• the identity of the labeled, blocked nucleotides incorporated into the copy strand during step 100 is then detected in the presence of the mixture of blocked, unlabeled nucleotides (130) in a“detection step.”
• the labeled, unblocked nucleotides may be incorporated into copy strands that are lagging and out of phase. That is, if a blocked, labeled nucleotide was not incorporated into the copy strand during step 100, a blocked, unlabeled nucleotide may be incorporated during the detection step 130 to bring lagging copy strands back into phase.
• the components of the composition comprising the blocked, unlabeled nucleotides should not substantially interfere with the detection of the identity of the incorporated labeled nucleotide.
• labeled nucleotides comprise fluorescent labels
• the components of the composition preferably do not produce a fluorescent signal under conditions that result in a fluorescent signal from the labeled nucleotides, and the components of the composition preferably do not interfere with the fluorescent signal produced by the labeled nucleotide.
• the time that the composition comprising the blocked, labeled nucleotides is incubated with the template strands during the detection step is preferably sufficient to reduce phasing.
• the length of the detection step is not increased to allow additional time for incorporation of the blocked, labeled nucleotides. That is, the duration of the detection steps is preferably a duration sufficient to detect the identity of the blocked, labeled nucleotide incorporated in the incorporation step.
• the duration of the detection steps is preferably a duration sufficient to detect the identity of the blocked, labeled nucleotide incorporated in the incorporation step.
• 90 second detection steps are often used with Illumina MiniSeqTM sequencers. However, it is believed that much shorter detection times may be sufficient to allow incorporation of nucleotides into lagging strands during the detection step.
• the time that the composition comprising the blocked, labeled nucleotides is incubated with the template strands during a detection step is between 5 seconds and 120 seconds, such as between 10 seconds and 90 seconds. In some embodiments, the time that the composition comprising the blocked, labeled nucleotides is incubated with the template strands during a detection step is 120 seconds or less, such as 60 seconds or less, 30 seconds or less, 10 seconds or less, or 5 seconds or less. In some embodiments, the time that the composition comprising the blocked, labeled nucleotides is incubated with the template strands during a detection step is 1 second or more, such as 5 seconds or more, or 10 seconds or more.
• the method may further include unblocking and un-labeling any labeled, blocked nucleotides incorporated into the copy strand in step 100 and unblocking any unlabeled, blocked nucleotides incorporated into the copy strand in step 130.
• the unblocking step involves removing a blocking moiety from the last incorporated nucleotide in the copy strand and the detectable moiety is cleaved from or masked on the last nucleotide incorporated into the copy strand.
• a wash step (not shown) may be performed between steps 130 and 140 or after step
• the process may be repeated until a predetermined number of cycles have been run or sequencing is completed.
• a mixture of blocked, labeled nucleotides, without a chain extending enzyme may be introduced to the site comprising the multiple template polynucleotide strands (150) and the process may be repeated, beginning at step 110.
• the chain extending enzyme may remain at the site.
• the chain extending enzyme be bound to the template strand, the copy strand or both, and may remain active for multiple sequencing cycles.
• a second chain extending enzyme which may be the same enzyme or a different enzyme from the first chain extending enzyme introduced at step 100, may be included with the composition comprising the mixture of blocked, unlabeled nucleotides and introduced to the site comprising the multiple template strands.
• Step 125 in FIG. 2 may replace step 120 in one or more cycles of the process of FIG. 1.
• a second chain extending enzyme is not added (e.g., as indicated in step 120 in FIG. 1) than if a second chain extending enzyme is added at step 125.
• the steps of nucleotide incorporation and detection can be repeated one or more times.
• the steps can be repeated at least 25 times in some embodiments, at least 75 times in other embodiments, and at least 100 times in yet other embodiments.
• the provided methods include, but are not limited to, repeating the incorporating and detection steps for a number of cycles in a range from between about 100 cycles to about 1,000 cycles, in some embodiments, from between about 100 cycles to about 500 cycles, in other embodiments, and from between about 100 cycles to about 300 cycles, in yet other embodiments.
• the sequencing methods described herein may be performed in any suitable manner, using any suitable equipment.
• the sequencing methods employ a solid support on which the multiple template polynucleotide strands are immobilized.
• immobilized as used herein is intended to encompass direct or indirect attachment to a solid support via covalent or non-covalent bond(s).
• all that is required is that the polynucleotides remain immobilized or attached to a support under conditions in which it is intended to use the support, for example in applications requiring nucleic acid amplification and/or sequencing.
• oligonucleotides or primers may be immobilized such that a 3’ end is available for enzymatic extension and/or at least a portion of the sequence is capable of hybridizing to a complementary sequence.
• Immobilization can occur via hybridization to a surface attached primer, in which case the immobilized primer or oligonucleotide may be in the 3’ -5’ orientation.
• immobilization may occur by non-base-pairing hybridization, such as the covalent attachment.
• the polynucleotides may be attached to the surface by hybridization or annealing to one or more primers in a patch of primers. Hybridization may be accomplished, for example, by ligating an adapter to the ends of the template polynucleotides.
• the nucleic acid sequence of the adapter can be complementary to the nucleic acid sequence of the primer, thus, allowing the adapter to bind or hybridize to the primer on the surface.
• the polynucleotides may be single- or double-stranded and adapters may be added to the 5’ and/or 3’ ends of the polynucleotides.
• the polynucleotides may be double-stranded, and adapters may be ligated onto the 3’ ends of double-stranded polynucleotide.
• polynucleotides may be used without any adapter.
• template polynucleotides may be attached to a surface by interactions other than hybridization to a complementary primer.
• a polynucleotide may be covalently attached to a surface using a chemical linkage such as those resulting from click chemistry or a receptor-ligand interaction such as streptavidin-biotin binding.
• Primer oligonucleotides, oligonucleotide primers and primers are used throughout interchangeably and are polynucleotide sequences that are capable of annealing specifically to one or more polynucleotide templates to be amplified or sequenced.
• primer oligonucleotides are single-stranded or partially single-stranded.
• Primers may also contain a mixture of non-natural bases, non-nucleotide chemical modifications or non-natural backbone linkages so long as the non-natural entities do not interfere with the function of the primer.
• a patch of primers on a surface of a solid support may comprise one or more different pluralities of primer molecules.
• a patch may comprise a first, second, third, fourth, or more pluralities of primer molecules each plurality having a different sequence.
• the different pluralities of primers may share a common sequence so long as there is a sequence difference between at least a portion of the different pluralities.
• a first plurality of primers may share a sequence with a second plurality of primers as long the primers in one plurality have a different sequence not found in the primers of the other plurality.
• the template polynucleotides may be amplified on the surface of the solid support.
• Polynucleotide amplification includes the process of amplifying or increasing the numbers of a polynucleotide template and/or of a complement thereof that are present, by producing one or more copies of the template and/or or its complement.
• Amplification may be carried out by a variety of known methods under conditions including, but not limited to, thermocycling amplification or isothermal amplification.
• methods for carrying out amplification are described in U.S. Publication No. 2009/0226975; WO 98/44151; WO 00/18957; WO 02/46456; WO 06/064199; and WO 07/010251; which are incorporated by reference herein in their entireties.
• amplification can occur on the surface to which the polynucleotide molecules are attached.
• This type of amplification can be referred to as solid phase amplification, which when used in reference to polynucleotides, refers to any polynucleotide amplification reaction carried out on or in association with a surface (e.g., a solid support).
• a surface e.g., a solid support
• all or a portion of the amplified products are synthesized by extension of an immobilized primer.
• Solid phase amplification reactions are analogous to standard solution phase amplifications except that at least one of the amplification primers is immobilized on a surface (e.g., a solid support).
• Suitable conditions include providing appropriate buffers/solutions for amplifying polynucleotides.
• Such solutions include, for example, an enzyme with polymerase activity, nucleotide triphosphates, and, optionally, additives such as DMSO or betaine.
• amplification is carried out in the presence of a recombinase agent as described in U.S. Patent No. 7,485,428, which is incorporated by reference herein in its entirety, which allows for amplification without thermal melting.
• recombinase agents such as the RecA protein from E.
• coli in the presence of, for example, ATP, dATP, ddATP, UTP, or ATPyS, will form a nucleoprotein filament around single-stranded DNA (e.g., a primer).
• a primer e.g., a primer
• the recombinase agent will catalyze a strand invasion reaction and pairing of the primer with the homologous strand of the target DNA.
• the original pairing strand is displaced by strand invasion leaving a bubble of single stranded DNA in the region, which serves as a template for amplification.
• Solid-phase amplification may comprise a polynucleotide amplification reaction comprising only one species of oligonucleotide primer immobilized to a surface.
• the surface may comprise a plurality of first and second different immobilized oligonucleotide primer species.
• Solid phase nucleic acid amplification reactions generally comprise at least one of two different types of nucleic acid amplification, interfacial and surface (or bridge) amplification.
• the solid support comprises a template polynucleotide that is indirectly immobilized to the solid support by hybridization to an immobilized oligonucleotide primer
• the immobilized primer may be extended in the course of a polymerase-catalyzed, template-directed elongation reaction (e.g ., primer extension) to generate an immobilized polynucleotide that remains attached to the solid support.
• the polynucleotides e.g., template and its complementary product
• the template polynucleotide may be made available in 1, 2, 3, 4, 5 or more rounds of primer extension or may be washed out of the reaction after 1, 2, 3, 4, 5 or more rounds of primer extension.
• an immobilized polynucleotide hybridizes to an immobilized oligonucleotide primer.
• the 3’ end of the immobilized polynucleotide provides the template for a polymerase-catalyzed, template-directed elongation reaction (e.g., primer extension) extending from the immobilized oligonucleotide primer.
• the resulting double-stranded product "bridges" the two primers and both strands are covalently attached to the support.
• both immobilized strands can serve as templates for new primer extension.
• Amplification may be used to produce colonies of immobilized polynucleotides.
• the methods can produce clustered arrays of polynucleotide colonies, analogous to those described in U.S. Patent No. 7,115,400; U.S. Publication No. 2005/0100900; WO 00/18957; and WO 98/44151, which are incorporated by reference herein in their entireties.
• Clusters” and “colonies” are used interchangeably and refer to a plurality of copies of a polynucleotide having the same sequence and/or complements thereof attached to a surface.
• the cluster comprises a plurality of copies of a polynucleotide having the same sequence and/or complements thereof, attached via their 5’ termini to the surface.
• the copies polynucleotides making up the clusters may be in a single or double stranded form.
• the plurality of template polynucleotides may be in a cluster, each cluster containing template polynucleotides of the same sequence.
• a plurality of clusters can be sequenced, each cluster comprising polynucleotides of the same sequence.
• the sequence of the polynucleotides in a first cluster is different from the sequence of the nucleic acid molecules of a second cluster.
• the cluster is formed by annealing to a primer on a solid surface a template polynucleotide and amplifying the template polynucleotide under conditions to form the cluster comprising the plurality of template polynucleotides of the same sequence.
• Amplification can be thermal or isothermal.
• Each colony may comprise polynucleotides of the same sequences.
• the sequence of the polynucleotides of one colony is different from the sequence of the polynucleotides of another colony.
• each colony comprises polynucleotides having different nucleic acid sequences. All the immobilized polynucleotides in a colony are typically produced by amplification of the same polynucleotide.
• a colony of immobilized polynucleotides contains one or more primers without an immobilized polynucleotide to which another polynucleotide of different sequence may bind upon additional application of solutions containing free or unbound polynucleotides.
• this second or invading polynucleotide may not amplify to significant numbers.
• the second or invading polynucleotide typically is less than 1, 0.5, 0.25, 0.1, 0.001 or 0.0001% of the total population of polynucleotides in a single colony.
• the second or invading polynucleotide may not be optically detected or detection of the second or invading polynucleotide is considered background noise or does not interfere with detection of the original, immobilized polynucleotides in the colony.
• the colony will be apparently homogeneous or uniform in accordance with the resolution of the methods or apparatus used to detect the colony.
• the clusters may have different shapes, sizes and densities depending on the conditions used.
• clusters may have a shape that is substantially round, multi-sided, donut-shaped or ring-shaped.
• the diameter or maximum cross section of a cluster may be from about 0.2 pm to about 6 pm, about 0.3 pm to about 4 pm, about 0.4 pm to about 3 pm, about 0.5 pm to about 2 pm, about 0.75 pm to about 1.5 pm, or any intervening diameter.
• the diameter or maximum cross section of a cluster may be at least about 0.5 pm, at least about 1 pm, at least about 1.5 pm, at least about 2 pm, at least about 2.5 pm, at least about 3 pm, at least about 4 pm, at least about 5 pm, or at least about 6 pm.
• the diameter of a cluster may be influenced by a number of parameters including, but not limited to, the number of amplification cycles performed in producing the cluster, the length of the polynucleotide template, the GC content of the polynucleotide template, the shape of a patch to which the primers are attached, or the density of primers attached to the surface upon which clusters are formed.
• the diameter of a cluster may be no larger than the patch upon which the cluster is formed. For example, if a patch is a bead, the cluster size will be no larger than the surface area of the bead.
• the density of clusters can be in the range of at least about 0.1/mm 2 , at least about 1/mm 2 , at least about 10/mm 2 , at least about 100/mm 2 , at least about 1,000/mm 2 , at least about 10,000/mm 2 to at least about 100,000/mm 2 .
• the clusters have a density of, for example, 100,000/mm 2 to 1,000,000/mm 2 or 1,000,000/mm 2 to 10,000,000/mm 2 .
• the methods provided herein can produce colonies that are of approximately equal size. This occurs regardless of the differences in efficiencies of amplification of the polynucleotides of different sequence.
• Clusters may be detected, for example, using a suitable imaging means, such as, a confocal imaging device or a charge coupled device (CCD) or CMOS camera.
• a suitable imaging means such as, a confocal imaging device or a charge coupled device (CCD) or CMOS camera.
• Exemplary imaging devices include, but are not limited to, those described in U.S. Patent Nos. 7,329,860; 5,754,291; and 5,981,956; and WO 2007/123744, each of which is herein incorporated by reference in its entirety.
• the imaging apparatus may be used to determine a reference position in a cluster or in a plurality of clusters on the surface, such as the location, boundary, diameter, area, shape, overlap and/or center of one or a plurality of clusters (and/or of a detectable signal originating therefrom). Such a reference position may be recorded, documented, annotated, converted into an interpretable signal, or the like, to yield meaningful information.
• support refers to a substrate for attaching polynucleotides.
• a support is a material having a rigid or semi-rigid surface to which a polynucleotide can be attached or upon which nucleic acids can be synthesized and/or modified.
• Supports can include any resin, gel, bead, well, column, chip, flowcell, membrane, matrix, plate, filter, glass, controlled pore glass (CPG), polymer support, membrane, paper, plastic, plastic tube or tablet, plastic bead, glass bead, slide, ceramic, silicon chip, multi-well plate, nylon membrane, fiber optic, and PVDF membrane.
• a support may include any flat wafer-like substrates and flat substrates having wells, such as a microtiter plate, including 96-well plates.
• Exemplary flat substrates include chips, slides, etched substrates, microtiter plates, and flow cell reactors, including multi-lane flow cell reactors having multiple microfluidic channels, such as the eight- channel flow cell used in the cBot sequencing workstation (Illumina, Inc., San Diego, CA).
• Exemplary flow cells are described in WO 2007/123744, which is incorporated herein by reference in its entirety.
• the flowcell is a patterned flowcell. Suitable patterned flowcells include, but are not limited to, flowcells described in WO 2008/157640, which is incorporated by reference herein in its entirety.
• a support may also include beads, including magnetic beads, hollow beads, and solid beads. Beads may be used in conjunction with flat supports, such flat supports optionally also containing wells. Beads, or alternatively microspheres, refer generally to a small body made of a rigid or semi-rigid material. The body may have a shape characterized, for example, as a sphere, oval, microsphere, or other recognized particle shape whether having regular or irregular dimensions.
• the sizes of beads include, without limitation, about 1 pm, about 2 pm, about 3 pm, about 5 pm, about 10 pm, about 20 pm, about 30 pm, about 40 pm, about 60 pm, about 100 pm, about 150 pm or about 200 pm in diameter.
• composition of a support may vary depending, for example, on the format, chemistry and/or method of attachment and/or on the method of nucleic acid synthesis.
• Support materials that can be used in accordance with the present disclosure include, but are not limited to, polypropylene, polyethylene, polybutylene, polyurethanes, nylon, metals, and other suitable materials.
• Exemplary compositions include supports, and chemical functionalities imparted thereto, used in polypeptide, polynucleotide and/or organic moiety synthesis.
• compositions include, for example, plastics, ceramics, glass, polystyrene, melamine, methylstyrene, acrylic polymers, paramagnetic materials, thoria sol, carbon graphite, titanium dioxide, latex or cross-linked dextrans such as SepharoseTM, cellulose, nylon, cross-linked micelles and TeflonTM, as well as any other materials which can be found described in, for example,“ Microsphere Detection Guide” from Bangs Laboratories, Fishers IN, which is incorporated herein by reference.
• a support particle may be made of cross-linked starch, dextrans, cellulose, proteins, organic polymers including styrene polymers including polystyrene and methylstyrene as well as other styrene co-polymers, plastics, glass, ceramics, acrylic polymers, magnetically responsive materials, colloids, thoriasol, carbon graphite, titanium dioxide, nylon, latex, or TEFLON®.
• "Microsphere Detection Guide” from Bangs Laboratories, Fishers, Inc. hereby incorporated by reference in its entirety, is a helpful guide.
• Further exemplary supports within the scope of the present disclosure include, for example, those described in US Application Publication No. 02/0102578 and U.S. Pat. No. 6,429,027, both of which are incorporated herein by reference in their entirety.
• a solid support 200 such as a flow cell
• the solid support 200 has a surface 210 to which clusters 300 containing multiple template polynucleotide strands having the same nucleotide sequence are bound.
• the surface 210 of the solid support 200 may be planar.
• Fluid compositions containing reagents, wash buffers, and the like may flow over the surface 210 of the solid support 200 to interact with the template polynucleotides in the clusters 300.
• the flow of the compositions may occur in any direction, such as the direction indicated by the arrows in FIG. 3.
• Sequencing apparatus with which the flow cell 300 may be used may be configured to flow reagents and compositions across the surface 210 to interact with the template strands in the clusters 300.
• the apparatus may cause chain extending enzymes, sequencing primers, nucleotides, wash compositions, unblocking reagents, un-labeling reagents, and the like to flow across the surface 210 of the solid support 200, such as a flow cell, to interact with the template polynucleotides in the clusters 300 at the appropriate times to carry out sequencing of the template strands.
• Each cluster 300 may contain the same template polynucleotides or different polynucleotides than another cluster 300.
• the template polynucleotides to be sequenced may be obtained from any biological sample using known, routine methods. Suitable biological samples include, but are not limited to, a blood sample, biopsy specimen, tissue explant, organ culture, biological fluid or any other tissue or cell preparation, or fraction or derivative thereof or isolated therefrom.
• the biological sample can be a primary cell culture or culture adapted cell line including but not limited to genetically engineered cell lines that may contain chromosomally integrated or episomal recombinant nucleic acid sequences, immortalized or immortalizable cell lines, somatic cell hybrid cell lines, differentiated or differentiatable cell lines, transformed cell lines, stem cells, germ cells (e.g. sperm, oocytes), transformed cell lines and the like.
• polynucleotide molecules may be obtained from primary cells, cell lines, freshly isolated cells or tissues, frozen cells or tissues, paraffin embedded cells or tissues, fixed cells or tissues, and/or laser dissected cells or tissues.
• Biological samples can be obtained from any subject or biological source including, for example, human or non-human animals, including mammals and non-mammals, vertebrates and invertebrates, and may also be any multicellular organism or single-celled organism such as a eukaryotic (including plants and algae) or prokaryotic organism, archaeon, microorganisms (e.g. bacteria, archaea, fungi, protists, viruses), and aquatic plankton.
• polynucleotides molecules of different sequence for use in the provided methods may be prepared using a variety of standard techniques available and known.
• Exemplary methods of polynucleotide molecule preparation include, but are not limited to, those described in Bentley et al, Nature 456:49-51 (2008); U.S. Patent No. 7,115,400; and U.S. Patent Application Publication Nos. 2007/0128624; 2009/0226975; 2005/0100900; 2005/0059048; 2007/0110638; and 2007/0128624, each of which is herein incorporated by reference in its entirety.
• the template polynucleotides may contain a variety of sequences including, but not limited to, universal sequences and known or unknown sequences.
• polynucleotide may comprise one or more regions of known sequence (e.g., an adaptor) located on the 5’ and/or 3’ ends.
• Such template polynucleotides may be formed by attaching adapters to the ends of a polynucleotides of unknown sequence.
• the polynucleotides comprise known sequences on the 5’ and 3’ ends, the known sequences may be the same or different sequences.
• a known sequence located on the 5’ and/or 3’ ends of the polynucleotides is capable of hybridizing to one or more primers immobilized on the surface.
• polynucleotide comprising a 5’ known sequence may hybridize to a first plurality of primers while the 3’ known sequence may hybridize to a second plurality of primers.
• polynucleotides comprise one or more detectable labels.
• the one or more detectable labels may be attached to the polynucleotide template at the 5’ end, at the 3’ end, and/or at any nucleotide position within the polynucleotide molecule.
• the polynucleotides for use in the provided methods may comprise the polynucleotide to be amplified and/or sequenced and, optionally, short nucleic acid sequences at the 5' and/or 3' end(s).
• a short nucleic acid sequence that is added to the 5’ and/or 3’ end of a polynucleotide may be a universal sequence.
• a universal sequence is a region of nucleotide sequence that is common to, i.e., shared by, two or more polynucleotides, where the two or more polynucleotides also have regions of sequence differences.
• a universal sequence that may be present in different members of a plurality of polynucleotides may allow the replication or amplification of multiple different sequences using a single universal primer that is complementary to the universal sequence.
• At least one, two (e.g., a pair) or more universal sequences that may be present in different members of a collection of polynucleotides may allow the replication or amplification of multiple different sequences using at least one, two (e.g., a pair) or more single universal primers that are complementary to the universal sequences.
• a universal primer includes a sequence that may hybridize specifically to such a universal sequence.
• the polynucleotide may be modified to attach universal adapters (e.g., non-target nucleic acid sequences) to one or both ends of the different target sequences, the adapters providing sites for hybridization of universal primers.
• This approach has the advantage that it is not necessary to design a specific pair of primers for each polynucleotide to be generated, amplified, sequenced, and/or otherwise analyzed; a single pair of primers can be used for amplification of different polynucleotides provided that each polynucleotide is modified by addition of the same universal primer-binding sequences to its 5' and 3' ends.
• polynucleotides may also be modified to include any nucleic acid sequence desirable using standard, known methods.
• additional sequences may include, for example, restriction enzyme sites, or indexing tags in order to permit identification of amplification products of a given nucleic acid sequence.
• the term different when used in reference to two or more polynucleotides means that the two or more polynucleotides have nucleotide sequences that are not the same.
• two polynucleotides can differ in the content and order of nucleotides in the sequence of one polynucleotide compared to the other polynucleotide.
• the term can be used to describe polynucleotides whether they are referred to as copies, amplicons, templates, targets, primers, oligonucleotides, or the like.
• FIGS. 4A-G schematic drawings illustrating an embodiment of a sequencing method is shown.
• the depicted embodiment illustrates a problem with phasing, and how the method addresses the problem.
• FIGS. 4A-G a plurality of polynucleotides 400 having the same sequence are shown.
• the polynucleotides 400 may be bound to a surface of a solid support at their 3’ or 5’ ends.
• the polynucleotides may be bound to the surface 210 in a cluster 300 on a flow cell 200 as depicted in FIG. 3.
• FIG. 4A shows the template polynucleotides 400 prior to the initiation of sequencing.
• FIG. 4B shows a single blocked, labeled nucleotide 510 incorporated into a copy strand 590 during a first round of sequencing, such as after the wash step 110 of FIGS. 1-2.
• the chain extending enzyme which may remain on the template polynucleotides 400 after a wash step, is not shown.
• a primer polynucleotide (not shown), complementary to a portion of the sequence of the template, may be used to facilitate incorporation of the nucleotides 510.
• a blocked, labeled nucleotide 510 is incorporated into copy strands 590 for four out of the five template polynucleotides 400. Without more, the strand in which no blocked, labeled nucleotide 510 was incorporated would be out of phase.
• a blocked, unlabeled nucleotide 515 could be incorporated into the lagging strand to bring the lagging strand into phase prior to the next cycle of sequencing.
• the blocked, unlabeled nucleotide 515 may be incorporated by a chain extending enzyme (not shown) that remains after a wash step (e.g., step 110 of FIGS. 1-2) or that is introduced with the mixture of unblocked, unlabeled nucleotides (e.g., step 125 of FIG. 2).
• the incorporated nucleotides 510, 515 may then be unblocked and unlabeled, in the case of nucleotides 510 (e.g., step 140 of FIGS. 1-2), and another cycle of sequencing may be performed.
• FIG. 4D shows incorporation of second blocked, labeled nucleotides 520 into the copy strand 590 following an incorporation step (such as step 100 of FIGS. 1-2) and a wash step (such as step 110 of FIGS. 1-2) in a second cycle of sequencing.
• a blocked, labeled nucleotide 520 is incorporated into copy strands 590 for four out of the five template polynucleotides 400. Without more, the copy strand 590 in which no blocked, labeled nucleotide 510 was incorporated would be out of phase.
• a blocked, unlabeled nucleotide 525 could be incorporated into the lagging strand to bring the lagging strand into phase prior to the next cycle of sequencing.
• the incorporated nucleotides 520, 525 may be unblocked and unlabeled, in the case of nucleotides 520 (e.g., step 140 of FIGS. 1-2) and another cycle of sequencing may be performed.
• FIG. 4F illustrates another cycle of sequencing in which blocked, labeled nucleotides
• FIG. 4G illustrates incorporation of a blocked, unlabeled nucleotide 535 into the lagging strand to bring the lagging strand into phase prior to the next cycle of sequencing.
• FIG. 4G illustrates incorporation of a blocked, unlabeled nucleotide 535 into the lagging strand to bring the lagging strand into phase prior to the next cycle of sequencing.
• all the copy strands 590 are in phase.
• three of the five strands would have been out of phase in the illustrated embodiment.
• the signal produced during the detection step would likely be too heterogeneous, due to incorporation of a different labeled nucleotide, to properly identify the appropriate nucleotide.
• FIGS. 4A-G are schematic, they illustrate a few key points.
• a small rate of phasing may be compounded over multiple cycles of sequencing.
• bringing lagging copy strands into phase during detection through the incorporation of unlabeled nucleotides does not require a great deal of chain extending activity due to the relatively low numbers of lagging strands after a round of incorporation.
• less than optimum conditions for incorporation of the unlabeled nucleotides may be tolerated for incorporation of the unlabeled nucleotides.
• conditions that are not intended to optimize the efficiency and accuracy of the chain extending enzyme may be tolerated.
• any suitable composition comprising the mixture of blocked, unlabeled nucleotides may be used.
• the composition comprises a buffered solution having a pH from about 8 to about 10, such as from about 9 to about 9.5.
• Any suitable buffer such as a Tris buffer, may be used.
• the blocked, unlabeled nucleotides may be present in any suitable concentration such as from about 0.001 to about 15 mM, such as from about 0.5 mM to about 5 mM, such as about 2 mM.
• the composition may comprise any suitable amount of a chelator, such as from about 0 mM to about 5 mM ethylenediaminetetraacetic acid (EDTA), or from about 0 mM to about 2 mM EDTA, or from about 0 mM to about 1 mM EDTA.
• a chelator such as from about 0 mM to about 5 mM ethylenediaminetetraacetic acid (EDTA), or from about 0 mM to about 2 mM EDTA, or from about 0 mM to about 1 mM EDTA.
• the composition may comprise any suitable amount of magnesium sulfate, such as from about 1 mM to about 10 mM MgSC> 4 , from about 2 mM to about 6 mM MgSC> 4 , or about 4 mM MgSC> 4 .
• the composition may comprise any suitable amount of a detergent.
• the composition may comprise from about 0.05% to about 1% detergent by weight, such as from about 0.1% to about 0.5% detergent by weight, or about 0.2% detergent by weight.
• Any suitable detergent may be used.
• polyoxyethylenesorbitan monolaurate also referred to as polyoxyethylenesorbitan monolaurate, or Tween
• CHAPS 3-[(3-cholamidopropyl)dimethylammonio]-l- propanesulfonate hydrate
• the composition may comprise any suitable amount of an antioxidant.
• the detergent may comprise one or more antioxidant in a combined total antioxidant concentration from about 1 mM to about 50 mM, such as from about 2 mM to about 40 mM, from about 3 mM to about 20 mM, or from about 15 mM to about 25 mM.
• Suitable antioxidants include ascorbate, acetovanillone, and Trolox.
• the composition is free of labeled nucleotides.
• the composition comprising a mixture of blocked, unlabeled nucleotides comprises a Tris buffer, has a pH of about 9 to about 9.5, has a detergent, MgSC>4, EDTA, ascorbate, and acetovanillone.
• the composition may include components as described in Table 1 below:
• Example 1 Increased phasing correlates with decreased incorporation time
• a polynucleotide of a known sequence was sequenced using an Illumina MiniSeqTM sequencer using, during the detection step, (i) the manufacturer’s scan mix (no blocked, unlabeled nucleotides and no polymerase - the“standard reagents”), and (ii) a modified scan mix that included blocked, unlabeled nucleotides and a polymerase [“ScanAndFill”].
• the ScanAndFill mix included polymerase Pol812.
• the other components of the ScanAndFill mixes were EA buffer; pH 9.85; MgS04; EDTA; A, C, and T nucleotide triphosphates modified to include a fluorescent dye with a cleavable LN3 linker as described, for example, in U.S. Published Patent Application Nos. 2013/0079232 and 2016/0040225 (A-LN3, C-LN3, and T-LN3); Dark (unlabeled) G, and CHAPS.
• An incorporation time of 7.5 seconds was used.
• Q30, phasing, and prephasing values at each cycle were calculated. “Q30” refers to the percentage of reads that pass the Q30 quality filter, i.e. an error rate of less of equal to 1 in 1000, or 0.1%. The results are presented in FIG. 7.
• pH may be varied and similar results may be obtained.

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